Bio-medical Imaging in Java Central

Biomedical
imaging software, manuals, documentation and presentations. Most are
implemented using ImageJ, the image processing program from
NIH written by Wayne Rasband.

DownloadingAll plugins and supporting libraries are in one file,
bij.jar. The only thing you need to access themis bij.jar and the plugin stub
files (otherwise ImageJ cannot find them)
in the plugins directory.

Register ROI and Register_ROI MI Edges for alignment of all slices in a stack to the first
slice. The MI stands for Mutual Information, the best performing registration
metric, and Edges stands for the use of edges - largest Hessian eigenvalue -
instead of gray values for improved performance. Implements affine
registration, i.e. only translation , rotation and scaling. It determines the
registration parameters from registration of the ROI, and then aligns the
full slice, so that for large images, you can define a small ROI (in an area
where there is a characteristic non-alignment or motion to correct for)
making it much faster.

Other plugins
have been implemented, but manuals are not available yet, and will be once
corresponding articles have been accepted. There is also some documentation
available on the ImageJ mailing list.Sources for these are for a while only available to anyone
making me a co-author.

RTA Reader plugin to read RTA Retinal Thickness
Analyzer maps, and Backprojection to
reconstruct a volume from a stack of projections at different angles.

NEW! HTTPCAM.EXE Finally, allows you to control
'any' camera on a Windows platform remotely. Currently only PVCAM cameras
(Roper Scientific) supported. A great way to use all
those different cameras : direct interfacing with ImageJ (JNI) is
difficult, but this server allows a standalone (lowcost) camera PC that you can
use as a box, no threat of updates to your regular system / software of
intruding on your camera acquisition, remote control of camera for long
experiments. I would like to set this up as an extension to ImageJ. Download and manual page

Run as an applet: here you can use all BIJ plugins
including VolumeJ, Surface and FlowJ without downloading and installing.
Allows opening and saving your own files.Also includes isosurface rendering algorithm, which is
about 100 times faster than previous algorithms and allows real-time
rendering. Design and implementation of this new, very fast, real time volume
rendering algorithm has been completed. See the applet and more information
at www.abramoff.net.

My thesis is available here in PDF format
(illustrations 72 dpi only). You will need the free Acrobat reader to view
it. It is also available in printed form on request. Its title is
"Objective Measurement of Motion in the Orbit". The purpose of my
thesis was to discover new techniques of measuring motion in soft tissues,
and determine their clinical benefit. The research included mathematical and
applied contributions to the measurement of optical flow in noisy and aliased
Magnetic Resonance images, the measurement of optical flow in
three-dimensional from 3-D image sequences, and from noisy and degraded 3-D
images, to the visualization of two- and three-dimensional optical flow
fields, and to image segmentation based on differential motion. It also included
clinical applications to 2-D and 3-D motion estimation in orbital tissues,
which lead to the discovery of the causes of both persistent pain after
orbital surgery and persistent diplopia after orbital surgery, a new
technique for non-invasive differentiation of benign and malignant orbital
tumors, and to the description of the orbital soft tissues as an organ of
gaze.